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Predicating macroscopic influences of drugs on human body, like efficacy and toxicity, is a central problem of small-molecule based drug discovery. Molecules can be represented as an undirected graph, and we can utilize graph convolution…
With the rise of social media, the spread of fake news has become a significant concern, potentially misleading public perceptions and impacting social stability. Although deep learning methods like CNNs, RNNs, and Transformer-based models…
Graph Neural Networks (GNNs) have emerged as the de facto standard for modeling graph data, with attention mechanisms and transformers significantly enhancing their performance on graph-based tasks. Despite these advancements, the…
Graph anomaly detection (GAD) has achieved success and has been widely applied in various domains, such as fraud detection, cybersecurity, finance security, and biochemistry. However, existing graph anomaly detection algorithms focus on…
Graph neural networks (GNNs), which propagate the node features through the edges and learn how to transform the aggregated features under label supervision, have achieved great success in supervised feature extraction for both node-level…
Machine learning (ML) and deep learning (DL) techniques have gained significant attention as reduced order models (ROMs) to computationally expensive structural analysis methods, such as finite element analysis (FEA). Graph neural network…
Gravitational-wave detection strategies are based on a signal analysis technique known as matched filtering. Despite the success of matched filtering, due to its computational cost, there has been recent interest in developing deep…
In recent years, graph neural networks (GNNs) have become a popular tool for solving various problems over graphs. In these models, the link structure of the graph is typically exploited and nodes' embeddings are iteratively updated based…
Graph neural networks (GNNs) have brought revolutionary advancements to the field of link prediction (LP), providing powerful tools for mining potential relationships in graphs. However, existing methods face challenges when dealing with…
Deep generative models have been praised for their ability to learn smooth latent representation of images, text, and audio, which can then be used to generate new, plausible data. However, current generative models are unable to work with…
Brain networks/graphs derived from resting-state functional MRI (fMRI) help study underlying pathophysiology of neurocognitive disorders by measuring neuronal activities in the brain. Some studies utilize learning-based methods for brain…
Graph neural networks (GNNs) face significant challenges with class imbalance, leading to biased inference results. To address this issue in heterogeneous graphs, we propose a novel framework that combines Graph Neural Network (GNN) and…
We study the challenges of applying deep learning to gene expression data. We find experimentally that there exists non-linear signal in the data, however is it not discovered automatically given the noise and low numbers of samples used in…
Accurate prediction of molecular properties is essential in drug discovery and related fields. However, existing graph neural networks (GNNs) often struggle to simultaneously capture both local and global molecular structures. In this work,…
Graph Neural Networks (GNNs) are characterized by their capacity of processing graph-structured data. However, due to the sparsity of labels under semi-supervised learning, they have been found to exhibit biased performance on specific…
We explore different strategies to integrate prior domain knowledge into the design of a deep neural network (DNN). We focus on graph neural networks (GNN), with a use case of estimating the potential energy of chemical systems (molecules…
Several works based on Generative Adversarial Networks (GAN) have been recently proposed to predict a set of medical images from a single modality (e.g, FLAIR MRI from T1 MRI). However, such frameworks are primarily designed to operate on…
The pre-training on the graph neural network model can learn the general features of large-scale networks or networks of the same type by self-supervised methods, which allows the model to work even when node labels are missing. However,…
The graph neural network (GNN) has been a powerful deep-learning tool in chemistry domain, due to its close connection with molecular graphs. Most GNN models collect and update atom and molecule features from the fed atom (and, in some…
This paper studies causal inference with observational data from a single large network. We consider a nonparametric model with interference in both potential outcomes and selection into treatment. Specifically, both stages may be the…